JAL-3490 revised layout and search algorithm (more tests to be added)

[jalview.git] / test / jalview / analysis / FinderTest.java

diff --git a/test/jalview/analysis/FinderTest.java b/test/jalview/analysis/FinderTest.java
index f3ae69f..43c48d0 100644 (file)
--- a/test/jalview/analysis/FinderTest.java
+++ b/test/jalview/analysis/FinderTest.java
@@ -71,8 +71,13 @@ public class FinderTest
     Cache.applicationProperties.setProperty("PAD_GAPS",
             Boolean.FALSE.toString());
 
-    String seqData = "seq1/8-18 ABCD--EF-GHIJI\n" + "seq2 A--BCDefHI\n"
-            + "seq3 --bcdEFH\n" + "seq4 aa---aMMMMMaaa\n";
+    //@formatter:off
+    String seqData = 
+        "seq1/8-18 ABCD--EF-GHIJI\n" + 
+        "seq2      A--BCDefHI\n" + 
+        "seq3      --bcdEFH\n" + 
+        "seq4      aa---aMMMMMaaa\n";
+    //@formatter:on
     af = new FileLoader().LoadFileWaitTillLoaded(seqData,
             DataSourceType.PASTE);
     av = af.getViewport();
@@ -95,7 +100,7 @@ public class FinderTest
      * find next match only
      */
     Finder f = new Finder(av);
-    f.findNext("E.H", false, false); // 'E, any character, H'
+    f.findNext("E.H", false, false, false); // 'E, any character, H'
     // should match seq2 efH only
     SearchResultsI sr = f.getSearchResults();
     assertEquals(sr.getSize(), 1);
@@ -105,7 +110,7 @@ public class FinderTest
     assertEquals(matches.get(0).getEnd(), 7);
 
     f = new Finder(av);
-    f.findAll("E.H", false, false); // 'E, any character, H'
+    f.findAll("E.H", false, false, false); // 'E, any character, H'
     // should match seq2 efH and seq3 EFH
     sr = f.getSearchResults();
     assertEquals(sr.getSize(), 2);
@@ -129,7 +134,7 @@ public class FinderTest
     /*
      * find first match should return seq1 residue 9
      */
-    f.findNext("9", false, false);
+    f.findNext("9", false, false, false);
     SearchResultsI sr = f.getSearchResults();
     assertEquals(sr.getSize(), 1);
     List<SearchResultMatchI> matches = sr.getResults();
@@ -141,7 +146,7 @@ public class FinderTest
      * find all matches should return seq1 and seq4 (others are too short)
      */
     f = new Finder(av);
-    f.findAll("9", false, false);
+    f.findAll("9", false, false, false);
     sr = f.getSearchResults();
     assertEquals(sr.getSize(), 2);
     matches = sr.getResults();
@@ -156,7 +161,7 @@ public class FinderTest
      * parsing of search string as integer is strict
      */
     f = new Finder(av);
-    f.findNext(" 9", false, false);
+    f.findNext(" 9", false, false, false);
     assertTrue(f.getSearchResults().isEmpty());
   }
 
@@ -167,25 +172,25 @@ public class FinderTest
   public void testFindNext()
   {
     /*
-     * start at second sequence; colIndex of -1
+     * start at second sequence; residueIndex of -1
      * means sequence id / description is searched
      */
     Finder f = new Finder(av);
     PA.setValue(f, "sequenceIndex", 1);
-    PA.setValue(f, "columnIndex", -1);
-    f.findNext("e", false, false); // matches id
+    PA.setValue(f, "residueIndex", -1);
+    f.findNext("e", false, false, false); // matches id
 
     assertTrue(f.getSearchResults().isEmpty());
     assertEquals(f.getIdMatches().size(), 1);
     assertSame(f.getIdMatches().get(0), al.getSequenceAt(1));
 
-    // colIndex is now 0 - for use in next find next
+    // residueIndex is now 0 - for use in next find next
     // searching A--BCDefHI
-    assertEquals(PA.getValue(f, "columnIndex"), 0);
+    assertEquals(PA.getValue(f, "residueIndex"), 0);
     f = new Finder(av);
     PA.setValue(f, "sequenceIndex", 1);
-    PA.setValue(f, "columnIndex", 0);
-    f.findNext("e", false, false); // matches in sequence
+    PA.setValue(f, "residueIndex", 0);
+    f.findNext("e", false, false, false); // matches in sequence
     assertTrue(f.getIdMatches().isEmpty());
     assertEquals(f.getSearchResults().getSize(), 1);
     List<SearchResultMatchI> matches = f.getSearchResults().getResults();
@@ -194,14 +199,14 @@ public class FinderTest
     assertSame(matches.get(0).getSequence(), al.getSequenceAt(1));
     // still in the second sequence
     assertEquals(PA.getValue(f, "sequenceIndex"), 1);
-    // next column position to search from is 7
-    assertEquals(PA.getValue(f, "columnIndex"), 7);
+    // next residue offset to search from is 5
+    assertEquals(PA.getValue(f, "residueIndex"), 5);
 
     // find next from end of sequence - finds next sequence id
     f = new Finder(av);
     PA.setValue(f, "sequenceIndex", 1);
-    PA.setValue(f, "columnIndex", 7);
-    f.findNext("e", false, false);
+    PA.setValue(f, "residueIndex", 7);
+    f.findNext("e", false, false, false);
     assertEquals(f.getIdMatches().size(), 1);
     assertSame(f.getIdMatches().get(0), al.getSequenceAt(2));
     assertTrue(f.getSearchResults().isEmpty());
@@ -223,7 +228,7 @@ public class FinderTest
      * find first match only
      */
     Finder f = new Finder(av2);
-    f.findNext("rAF", false, true);
+    f.findNext("rAF", false, true, false);
     assertEquals(f.getIdMatches().size(), 1);
     assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0));
     assertTrue(f.getSearchResults().isEmpty());
@@ -232,7 +237,7 @@ public class FinderTest
      * find all matches
      */
     f = new Finder(av2);
-    f.findAll("rAF", false, true);
+    f.findAll("rAF", false, true, false);
     assertEquals(f.getIdMatches().size(), 2);
     assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0));
     assertSame(f.getIdMatches().get(1), al2.getSequenceAt(1));
@@ -242,7 +247,7 @@ public class FinderTest
      * case sensitive
      */
     f = new Finder(av2);
-    f.findAll("RAF", true, true);
+    f.findAll("RAF", true, true, false);
     assertEquals(f.getIdMatches().size(), 1);
     assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0));
     assertTrue(f.getSearchResults().isEmpty());
@@ -258,7 +263,7 @@ public class FinderTest
     /*
      * sequence matches should have no duplicates
      */
-    f.findAll("EFH", false, true);
+    f.findAll("EFH", false, true, false);
     assertEquals(f.getIdMatches().size(), 2);
     assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0));
     assertSame(f.getIdMatches().get(1), al2.getSequenceAt(1));
@@ -286,7 +291,7 @@ public class FinderTest
      * case insensitive; seq1 occurs twice in sequence id but
      * only one match should be returned
      */
-    f.findAll("SEQ1", false, false);
+    f.findAll("SEQ1", false, false, false);
     assertEquals(f.getIdMatches().size(), 1);
     assertSame(f.getIdMatches().get(0), al.getSequenceAt(0));
     SearchResultsI searchResults = f.getSearchResults();
@@ -296,7 +301,7 @@ public class FinderTest
      * case sensitive
      */
     f = new Finder(av);
-    f.findAll("SEQ1", true, false);
+    f.findAll("SEQ1", true, false, false);
     searchResults = f.getSearchResults();
     assertTrue(searchResults.isEmpty());
 
@@ -307,7 +312,7 @@ public class FinderTest
     AlignViewportI av2 = new AlignViewport(al2);
     al2.addSequence(new Sequence("aBz", "xyzabZpqrAbZ"));
     f = new Finder(av2);
-    f.findAll("ABZ", false, false);
+    f.findAll("ABZ", false, false, false);
     assertEquals(f.getIdMatches().size(), 1);
     assertSame(f.getIdMatches().get(0), al2.getSequenceAt(4));
     searchResults = f.getSearchResults();
@@ -328,11 +333,15 @@ public class FinderTest
   @Test(groups = "Functional")
   public void testFind_findNext()
   {
+    // "seq1/8-18 ABCD--EF-GHIJI\n" +
+    // "seq2 A--BCDefHI\n" +
+    // "seq3 --bcdEFH\n" +
+    // "seq4 aa---aMMMMMaaa\n";
     /*
      * efh should be matched in seq2 only
      */
     FinderI f = new Finder(av);
-    f.findNext("EfH", false, false);
+    f.findNext("EfH", false, false, false);
     SearchResultsI searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
     SearchResultMatchI match = searchResults.getResults().get(0);
@@ -344,7 +353,7 @@ public class FinderTest
      * I should be found in seq1 (twice) and seq2 (once)
      */
     f = new Finder(av);
-    f.findNext("I", false, false); // find next: seq1/16
+    f.findNext("I", false, false, false); // find next: seq1/16
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
     match = searchResults.getResults().get(0);
@@ -352,7 +361,7 @@ public class FinderTest
     assertEquals(match.getStart(), 16);
     assertEquals(match.getEnd(), 16);
 
-    f.findNext("I", false, false); // find next: seq1/18
+    f.findNext("I", false, false, false); // find next: seq1/18
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
     match = searchResults.getResults().get(0);
@@ -360,7 +369,7 @@ public class FinderTest
     assertEquals(match.getStart(), 18);
     assertEquals(match.getEnd(), 18);
 
-    f.findNext("I", false, false); // find next: seq2/8
+    f.findNext("I", false, false, false); // find next: seq2/8
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
     match = searchResults.getResults().get(0);
@@ -368,13 +377,13 @@ public class FinderTest
     assertEquals(match.getStart(), 8);
     assertEquals(match.getEnd(), 8);
 
-    f.findNext("I", false, false);
+    f.findNext("I", false, false, false);
     assertTrue(f.getSearchResults().isEmpty());
 
     /*
      * find should reset to start of alignment after a failed search
      */
-    f.findNext("I", false, false); // find next: seq1/16
+    f.findNext("I", false, false, false); // find next: seq1/16
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
     match = searchResults.getResults().get(0);
@@ -391,7 +400,7 @@ public class FinderTest
   public void testFind_maximalResultOnly()
   {
     Finder f = new Finder(av);
-    f.findAll("M+", false, false);
+    f.findAll("M+", false, false, false);
     SearchResultsI searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
     SearchResultMatchI match = searchResults.getResults().get(0);
@@ -404,10 +413,10 @@ public class FinderTest
    * Test finding all matches of a sequence pattern in an alignment
    */
   @Test(groups = "Functional")
-  public void testFind_findAll()
+  public void testFindAll()
   {
     Finder f = new Finder(av);
-    f.findAll("EfH", false, false);
+    f.findAll("EfH", false, false, false);
     SearchResultsI searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 2);
     SearchResultMatchI match = searchResults.getResults().get(0);
@@ -422,7 +431,7 @@ public class FinderTest
     /*
      * find all I should find 2 positions in seq1, 1 in seq2
      */
-    f.findAll("I", false, false);
+    f.findAll("I", false, false, false);
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 3);
     match = searchResults.getResults().get(0);
@@ -450,7 +459,7 @@ public class FinderTest
     /*
      * BC should match seq1/9-10 and seq2/2-3
      */
-    f.findAll("BC", true, false);
+    f.findAll("BC", true, false, false);
     SearchResultsI searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 2);
     SearchResultMatchI match = searchResults.getResults().get(0);
@@ -466,7 +475,7 @@ public class FinderTest
      * bc should match seq3/1-2
      */
     f = new Finder(av);
-    f.findAll("bc", true, false);
+    f.findAll("bc", true, false, false);
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
     match = searchResults.getResults().get(0);
@@ -474,7 +483,7 @@ public class FinderTest
     assertEquals(match.getStart(), 1);
     assertEquals(match.getEnd(), 2);
 
-    f.findAll("bC", true, false);
+    f.findAll("bC", true, false, false);
     assertTrue(f.getSearchResults().isEmpty());
   }
 
@@ -497,7 +506,7 @@ public class FinderTest
     av.setSelectionGroup(sg);
 
     FinderI f = new Finder(av);
-    f.findNext("b", false, false);
+    f.findNext("b", false, false, false);
     assertTrue(f.getIdMatches().isEmpty());
     SearchResultsI searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
@@ -509,12 +518,12 @@ public class FinderTest
     /*
      * a second Find should not return the 'b' in seq3 as outside the selection
      */
-    f.findNext("b", false, false);
+    f.findNext("b", false, false, false);
     assertTrue(f.getSearchResults().isEmpty());
     assertTrue(f.getIdMatches().isEmpty());
 
     f = new Finder(av);
-    f.findNext("d", false, false);
+    f.findNext("d", false, false, false);
     assertTrue(f.getIdMatches().isEmpty());
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
@@ -522,7 +531,7 @@ public class FinderTest
     assertSame(match.getSequence(), al.getSequenceAt(1));
     assertEquals(match.getStart(), 4);
     assertEquals(match.getEnd(), 4);
-    f.findNext("d", false, false);
+    f.findNext("d", false, false, false);
     assertTrue(f.getIdMatches().isEmpty());
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
@@ -554,7 +563,7 @@ public class FinderTest
      * search for 'e' should match two sequence ids and one residue
      */
     Finder f = new Finder(av);
-    f.findAll("e", false, false);
+    f.findAll("e", false, false, false);
     assertEquals(f.getIdMatches().size(), 2);
     assertSame(f.getIdMatches().get(0), al.getSequenceAt(1));
     assertSame(f.getIdMatches().get(1), al.getSequenceAt(2));
@@ -569,7 +578,7 @@ public class FinderTest
      * search for 'Q' should match two sequence ids only
      */
     f = new Finder(av);
-    f.findAll("Q", false, false);
+    f.findAll("Q", false, false, false);
     assertEquals(f.getIdMatches().size(), 2);
     assertSame(f.getIdMatches().get(0), al.getSequenceAt(1));
     assertSame(f.getIdMatches().get(1), al.getSequenceAt(2));
@@ -600,7 +609,7 @@ public class FinderTest
      * search for 'I' should match two sequence positions
      */
     Finder f = new Finder(av);
-    f.findAll("I", false, false);
+    f.findAll("I", false, false, false);
     assertTrue(f.getIdMatches().isEmpty());
     SearchResultsI searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 2);
@@ -637,7 +646,7 @@ public class FinderTest
     hc.hideColumns(3, 3);
     al.setHiddenColumns(hc);
     Finder f = new Finder(av);
-    f.findAll("aaa", false, false);
+    f.findAll("aaa", false, false, false);
     SearchResultsI searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 2);
     SearchResultMatchI match = searchResults.getResults().get(0);
@@ -659,7 +668,7 @@ public class FinderTest
      * find the visible D in seq2
      */
     f = new Finder(av);
-    f.findAll("D", false, false);
+    f.findAll("D", false, false, false);
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
     match = searchResults.getResults().get(0);
@@ -672,7 +681,7 @@ public class FinderTest
      * consecutive in the visible columns
      */
     f = new Finder(av);
-    f.findAll("AD", false, false);
+    f.findAll("AD", false, false, false);
     searchResults = f.getSearchResults();
     assertTrue(searchResults.isEmpty());
 
@@ -681,7 +690,7 @@ public class FinderTest
      * (first run includes hidden gaps)
      */
     f = new Finder(av);
-    f.findAll("aaa", false, false);
+    f.findAll("aaa", false, false, false);
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 2);
     match = searchResults.getResults().get(0);
@@ -695,23 +704,27 @@ public class FinderTest
 
     /*
      * hide columns 2-5:
-     * find all 'aaa' should find end of seq4 only
-     * (hidden columns not all gapped)
+     * find all 'aaa' should match twice in seq4
+     * (first match partly hidden, second all visible)
      */
     hc.hideColumns(2, 5);
     f = new Finder(av);
-    f.findAll("aaa", false, false);
+    f.findAll("aaa", false, false, false);
     searchResults = f.getSearchResults();
-    assertEquals(searchResults.getSize(), 1);
+    assertEquals(searchResults.getSize(), 2);
     match = searchResults.getResults().get(0);
     assertSame(match.getSequence(), al.getSequenceAt(3));
+    assertEquals(match.getStart(), 1);
+    assertEquals(match.getEnd(), 3);
+    match = searchResults.getResults().get(1);
+    assertSame(match.getSequence(), al.getSequenceAt(3));
     assertEquals(match.getStart(), 9);
     assertEquals(match.getEnd(), 11);
 
     /*
      * find all 'BE' should not match across hidden columns in seq1
      */
-    f.findAll("BE", false, false);
+    f.findAll("BE", false, false, false);
     assertTrue(f.getSearchResults().isEmpty());
 
     /*
@@ -721,7 +734,7 @@ public class FinderTest
     hc.revealAllHiddenColumns(new ColumnSelection());
     hc.hideColumns(8, 13);
     f = new Finder(av);
-    f.findNext("H", false, false);
+    f.findNext("H", false, false, false);
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
     match = searchResults.getResults().get(0);
@@ -764,7 +777,7 @@ public class FinderTest
      * should match seq2/1, seq2/7, not seq3/6
      */
     Finder f = new Finder(av);
-    f.findAll("[AH]", false, false);
+    f.findAll("[AH]", false, false, false);
     SearchResultsI searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 2);
     SearchResultMatchI match = searchResults.getResults().get(0);